Multiple sequence alignment - TraesCS4A01G374200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4A01G374200 chr4A 100.000 3659 0 0 1 3659 649006564 649010222 0.000000e+00 6758.0
1 TraesCS4A01G374200 chr4A 96.866 3670 102 5 1 3659 649056239 649059906 0.000000e+00 6128.0
2 TraesCS4A01G374200 chr4A 90.243 3044 237 28 550 3562 657307370 657310384 0.000000e+00 3921.0
3 TraesCS4A01G374200 chr4A 90.210 3044 237 30 550 3562 657367064 657370077 0.000000e+00 3914.0
4 TraesCS4A01G374200 chr4A 90.134 3051 237 28 550 3562 649144898 649147922 0.000000e+00 3908.0
5 TraesCS4A01G374200 chr4A 90.226 2701 216 23 550 3216 649184181 649186867 0.000000e+00 3482.0
6 TraesCS4A01G374200 chr4A 90.294 1566 121 16 550 2093 649174373 649175929 0.000000e+00 2021.0
7 TraesCS4A01G374200 chr4A 87.618 638 44 16 2936 3560 649175927 649176542 0.000000e+00 708.0
8 TraesCS4A01G374200 chr4A 90.058 342 24 4 3233 3565 649195951 649196291 5.610000e-118 435.0
9 TraesCS4A01G374200 chr4A 81.659 229 27 7 318 545 649143744 649143958 3.760000e-40 176.0
10 TraesCS4A01G374200 chr4A 84.663 163 10 8 391 550 657306287 657306437 8.190000e-32 148.0
11 TraesCS4A01G374200 chr4A 84.663 163 10 7 391 550 657365982 657366132 8.190000e-32 148.0
12 TraesCS4A01G374200 chr7D 93.634 2969 135 23 448 3375 41817896 41820851 0.000000e+00 4386.0
13 TraesCS4A01G374200 chr7D 90.535 3064 206 38 553 3559 42212736 42215772 0.000000e+00 3975.0
14 TraesCS4A01G374200 chr7D 90.241 3033 199 34 572 3562 42246217 42249194 0.000000e+00 3871.0
15 TraesCS4A01G374200 chr7D 91.434 2720 172 22 553 3241 42084286 42081597 0.000000e+00 3675.0
16 TraesCS4A01G374200 chr7D 92.137 2569 175 15 645 3199 42427414 42429969 0.000000e+00 3600.0
17 TraesCS4A01G374200 chr7D 91.142 2574 176 20 553 3104 41916899 41914356 0.000000e+00 3443.0
18 TraesCS4A01G374200 chr7D 91.379 406 30 4 1 404 41817500 41817902 5.340000e-153 551.0
19 TraesCS4A01G374200 chr7D 91.228 342 19 5 3233 3565 42435549 42435888 4.310000e-124 455.0
20 TraesCS4A01G374200 chr7D 87.500 312 21 9 550 846 42422941 42423249 9.730000e-91 344.0
21 TraesCS4A01G374200 chr7D 90.435 230 21 1 318 546 42244934 42245163 5.940000e-78 302.0
22 TraesCS4A01G374200 chr7D 84.746 236 22 6 318 551 42211567 42211790 1.320000e-54 224.0
23 TraesCS4A01G374200 chr7D 83.468 248 27 6 318 563 41918066 41917831 6.150000e-53 219.0
24 TraesCS4A01G374200 chr7D 86.420 162 9 7 9 157 42114131 42113970 8.130000e-37 165.0
25 TraesCS4A01G374200 chr7B 90.443 3045 232 25 553 3565 2564079 2561062 0.000000e+00 3956.0
26 TraesCS4A01G374200 chr7A 90.049 3055 238 29 550 3562 41626228 41629258 0.000000e+00 3897.0
27 TraesCS4A01G374200 chr7A 89.566 3067 241 33 550 3551 41619260 41622312 0.000000e+00 3818.0
28 TraesCS4A01G374200 chr7A 92.034 2586 174 15 647 3216 41746700 41749269 0.000000e+00 3605.0
29 TraesCS4A01G374200 chr7A 91.915 2585 180 13 647 3216 41775205 41777775 0.000000e+00 3589.0
30 TraesCS4A01G374200 chr7A 91.802 2586 179 15 647 3216 41716265 41718833 0.000000e+00 3570.0
31 TraesCS4A01G374200 chr7A 91.014 345 17 8 3233 3565 41791230 41791572 1.550000e-123 453.0
32 TraesCS4A01G374200 chr7A 93.651 63 4 0 9 71 41472855 41472917 1.080000e-15 95.3
33 TraesCS4A01G374200 chr2B 91.111 2610 201 13 553 3142 783889112 783886514 0.000000e+00 3506.0
34 TraesCS4A01G374200 chrUn 89.482 1255 91 14 2324 3562 361890052 361891281 0.000000e+00 1548.0
35 TraesCS4A01G374200 chrUn 85.128 195 14 7 359 550 392891474 392891656 6.240000e-43 185.0
36 TraesCS4A01G374200 chrUn 83.636 165 15 6 3410 3565 250930290 250930129 1.060000e-30 145.0
37 TraesCS4A01G374200 chrUn 83.951 162 14 6 3410 3562 283093503 283093661 1.060000e-30 145.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4A01G374200 chr4A 649006564 649010222 3658 False 6758.0 6758 100.0000 1 3659 1 chr4A.!!$F1 3658
1 TraesCS4A01G374200 chr4A 649056239 649059906 3667 False 6128.0 6128 96.8660 1 3659 1 chr4A.!!$F2 3658
2 TraesCS4A01G374200 chr4A 649184181 649186867 2686 False 3482.0 3482 90.2260 550 3216 1 chr4A.!!$F3 2666
3 TraesCS4A01G374200 chr4A 649143744 649147922 4178 False 2042.0 3908 85.8965 318 3562 2 chr4A.!!$F5 3244
4 TraesCS4A01G374200 chr4A 657306287 657310384 4097 False 2034.5 3921 87.4530 391 3562 2 chr4A.!!$F7 3171
5 TraesCS4A01G374200 chr4A 657365982 657370077 4095 False 2031.0 3914 87.4365 391 3562 2 chr4A.!!$F8 3171
6 TraesCS4A01G374200 chr4A 649174373 649176542 2169 False 1364.5 2021 88.9560 550 3560 2 chr4A.!!$F6 3010
7 TraesCS4A01G374200 chr7D 42081597 42084286 2689 True 3675.0 3675 91.4340 553 3241 1 chr7D.!!$R1 2688
8 TraesCS4A01G374200 chr7D 42427414 42429969 2555 False 3600.0 3600 92.1370 645 3199 1 chr7D.!!$F2 2554
9 TraesCS4A01G374200 chr7D 41817500 41820851 3351 False 2468.5 4386 92.5065 1 3375 2 chr7D.!!$F4 3374
10 TraesCS4A01G374200 chr7D 42211567 42215772 4205 False 2099.5 3975 87.6405 318 3559 2 chr7D.!!$F5 3241
11 TraesCS4A01G374200 chr7D 42244934 42249194 4260 False 2086.5 3871 90.3380 318 3562 2 chr7D.!!$F6 3244
12 TraesCS4A01G374200 chr7D 41914356 41918066 3710 True 1831.0 3443 87.3050 318 3104 2 chr7D.!!$R3 2786
13 TraesCS4A01G374200 chr7B 2561062 2564079 3017 True 3956.0 3956 90.4430 553 3565 1 chr7B.!!$R1 3012
14 TraesCS4A01G374200 chr7A 41619260 41629258 9998 False 3857.5 3897 89.8075 550 3562 2 chr7A.!!$F6 3012
15 TraesCS4A01G374200 chr7A 41746700 41749269 2569 False 3605.0 3605 92.0340 647 3216 1 chr7A.!!$F3 2569
16 TraesCS4A01G374200 chr7A 41775205 41777775 2570 False 3589.0 3589 91.9150 647 3216 1 chr7A.!!$F4 2569
17 TraesCS4A01G374200 chr7A 41716265 41718833 2568 False 3570.0 3570 91.8020 647 3216 1 chr7A.!!$F2 2569
18 TraesCS4A01G374200 chr2B 783886514 783889112 2598 True 3506.0 3506 91.1110 553 3142 1 chr2B.!!$R1 2589
19 TraesCS4A01G374200 chrUn 361890052 361891281 1229 False 1548.0 1548 89.4820 2324 3562 1 chrUn.!!$F2 1238

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
249 251 0.625849 CCCCACTTATTGAGGGCTGT 59.374 55.000 0.0 0.0 44.08 4.40 F
1473 9528 1.871039 AGTTTTTCGGGTGATGTCGTG 59.129 47.619 0.0 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 10107 0.804364 TTCGCAGCCATCACAATGAC 59.196 50.000 0.0 0.0 34.61 3.06 R
2769 10867 1.675641 GAGGCAGAACAACCCGCAT 60.676 57.895 0.0 0.0 0.00 4.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 5.659463 TGCAAGCAAGTTGTTCAAATAACT 58.341 33.333 4.48 0.00 41.31 2.24
136 137 9.191479 AGATGAACTAGCTATTAGTGTTACTGT 57.809 33.333 0.00 0.00 41.80 3.55
249 251 0.625849 CCCCACTTATTGAGGGCTGT 59.374 55.000 0.00 0.00 44.08 4.40
415 418 4.359434 TTCCATGTACAGGCTTACAACA 57.641 40.909 0.96 2.95 35.60 3.33
424 427 8.039603 TGTACAGGCTTACAACATTCTTATTG 57.960 34.615 0.00 0.00 0.00 1.90
549 562 7.663081 GGATGGCTATGTCTTGAGAAATAATCA 59.337 37.037 0.00 2.09 0.00 2.57
781 8827 8.321353 CCCTATAATGTATCAGGACATGCTTTA 58.679 37.037 0.00 0.00 39.99 1.85
948 9002 3.510719 TCAAGCAAACAAGCAAACACTC 58.489 40.909 0.00 0.00 36.85 3.51
1299 9354 5.542635 TCAACCCAAGTATCTCACTAGTGTT 59.457 40.000 21.99 11.06 36.04 3.32
1473 9528 1.871039 AGTTTTTCGGGTGATGTCGTG 59.129 47.619 0.00 0.00 0.00 4.35
2677 10775 8.660373 CCGGCTAAATTATCTAATCAGTGAATC 58.340 37.037 0.00 0.00 0.00 2.52
2752 10850 0.037790 GAGATCCGATGCTGGGCTAC 60.038 60.000 0.00 0.00 0.00 3.58
2825 10923 5.807520 CCACTGAGTTGTATGATGTACTGTC 59.192 44.000 0.00 0.00 0.00 3.51
3562 11736 1.768275 TCTCAGAACCACCTTCAGCAA 59.232 47.619 0.00 0.00 0.00 3.91
3579 11753 1.896660 AATTCGTGTTGCGCTGGGT 60.897 52.632 9.73 0.00 41.07 4.51
3626 11800 1.810532 GTCTCCTACACCTCCAGCG 59.189 63.158 0.00 0.00 0.00 5.18
3627 11801 0.680280 GTCTCCTACACCTCCAGCGA 60.680 60.000 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 9.804758 AACAGTAACACTAATAGCTAGTTCATC 57.195 33.333 0.00 0.00 38.92 2.92
198 199 2.286523 CCGCACCAGAGGAGGAAGT 61.287 63.158 0.00 0.00 36.74 3.01
249 251 3.492656 GGAATGTTAGCCTCGCATGACTA 60.493 47.826 0.00 0.00 0.00 2.59
301 303 2.745281 GGTATTTGCAAACTACAGCCGA 59.255 45.455 15.41 0.00 0.00 5.54
308 310 3.505680 CAGGTGCTGGTATTTGCAAACTA 59.494 43.478 15.41 5.69 41.10 2.24
415 418 4.641989 CACTACCAGCCAAGCAATAAGAAT 59.358 41.667 0.00 0.00 0.00 2.40
424 427 1.537202 CAAGAACACTACCAGCCAAGC 59.463 52.381 0.00 0.00 0.00 4.01
574 1627 7.643764 CGTCACAAATTACTTGTCACAGAAATT 59.356 33.333 0.00 0.00 45.50 1.82
781 8827 5.250200 TCTAAATATTGAACCGTTGGTGCT 58.750 37.500 0.00 0.00 35.34 4.40
948 9002 1.754234 GGTGCAATGGTAGGCTGGG 60.754 63.158 0.00 0.00 0.00 4.45
1473 9528 3.329386 TGACTTGTAGCTTGATGAGTGC 58.671 45.455 0.00 0.00 0.00 4.40
1696 9771 2.095461 GAAATTTCCCTCTGCCCACTC 58.905 52.381 6.95 0.00 0.00 3.51
1799 9884 9.953697 TTAGTTGTTTCTGCACGTTATAAAATT 57.046 25.926 0.00 0.00 0.00 1.82
2018 10107 0.804364 TTCGCAGCCATCACAATGAC 59.196 50.000 0.00 0.00 34.61 3.06
2426 10518 5.846203 AGCAGATTTAACAATTGTTGCACT 58.154 33.333 29.72 19.98 38.90 4.40
2642 10740 5.794894 AGATAATTTAGCCGGACATAGTGG 58.205 41.667 5.05 0.00 0.00 4.00
2769 10867 1.675641 GAGGCAGAACAACCCGCAT 60.676 57.895 0.00 0.00 0.00 4.73
3579 11753 0.390603 CGGATCCAGCACCGTACAAA 60.391 55.000 13.41 0.00 43.53 2.83
3601 11775 2.102553 GTGTAGGAGACGAGGCGC 59.897 66.667 0.00 0.00 0.00 6.53
3639 11813 2.101209 GACGCACCGTGTTGACCTTG 62.101 60.000 0.00 0.00 41.37 3.61


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.